I think the issue is that because you're using two indexes, both of which can be called in any loop iteration (but aren't, in reality) Matlab is having a hard time understanding the structure of your variables. Try this and see if it works:
parfor index1 = 1:Nx
trunc_i = NaN(1,Ny);
for index2 = 1:Ny
%Stuff
[trunc_i(index2),%Stuff] = predictor_precompute_eastwest(qstar,qeast,qwest,qstar,data,cellcenter);
speedmaxF(iv1ghost) = max([speedmaxF(iv1ghost) maxspeedF]);
end
trunc_east(index1,:) = trunc_i;
end
Basically, try using a temporary variable inside the inner loop to store the values you need to assign to trunc_east then assign it only once at the end of the outer loop.
You'll have to to do the same thing with your other variables as well.
I'd had success with this in the past; hopefully it will work here.
